Structure of proteins-

Structure of proteins- Proteins are polymers of L- amino acids.

Primary - The sequence of consecutive amino acid in a polypeptide chain  which are covelently joined by peptide bond. Starts from amino terminal and ends with carboxyl terminal.

                                                         Image source-https://biochemanics.files.wordpress.com/2013/04/protein_-_primary_structure.jpg

2.Secondary structure- The aminoacids of peptide chain fold in repeted fashion . Sequence of amio acids are joined by H- bonds. Formation of 3 forms-

 a.alpha helix-

•  Helix is  looks like a spiral structure(telephone cord shape) with 3.6 aminoacid per turn. 
• It is stabilized by H-bond between carbonyl oxygen and amide nitrogen.  
• The alpha helix is about 11 aa long.
•  It can be right or left handed but mostly right handed in proteins .
• The rise per residue is 1.5 A.
• The pitch( rise per turn ) is 3.6 x1.5 A= 0.54nm or 5.4 A.The stability of an α-helix is affected by the identity of the side chains.
• The amino acid residues in the helix have conformations with psi= (-45 to -50) and phi =-60
• Average length=12 amino acids (3 turns) 18 A
• Bonding of C-O with N-H at n+4. R points outwards and downwards.

CONSTRAINTS WHICH AFFECT  ALPHA HELIX STABILITY -
A.The electrostatic repulsion
B.Bulkiness of R group
C.Occurance of pro and gly residues.

b.beta pleted sheets - 

•  It is fully extended and pleated structure. 
• Beta strands organized next to each other and make beta sheets.       
•  Found in both fibrous and globular proteins.
• Stabilized by H-bonds between peptide chains.
• These interactions do not involve side chains.
• Distance between adjacent aminoacid is 3.5A.
• It is of  2 types parallel (run in same direction )and antiparallel (run in opposite directions).In an antiparallel arrangement, the successive β-strands alternate directions so that the N-terminus of one strand is adjacent to the C-terminus of the next.  The antiparallel beta strands its called secondary motif beta hairpin. The loop between 2beta strands are called beta turn .
• Beta sheets are usually twisted rather than flat .

A.antiparallel B.Parallel

https://www.studyblue.com/notes/note/n/ch-6-amino-acids-and-protein-structure/deck/16622904

c.BETA BEND/LOOPS -

• Polypeptide chains fold upon themselves forming a bend or loop.
• Bends are usally in the surface of globular proteins.

Glycine is small and flexible and occur frequently .

• Proline residues found in the bends / loops .

Tertiary structure -

• 3D folding.
• Non polar residues are buried inside polar residues exposed outwards .
• Many proteins are organized into multiple domains.
• Different protein may share different domain structure.
• 5 kinds of bonds stabilize tertiary structure -( H-bonds,Vanderwall interactions,Hydrophobic interactions,Ionic interactions and Disulphide linkages.)
• Quaternary structure -
• More than one polypeptide chains.
• Oligomeric proteins are involved.
• Stabilized by disulphide bond.

Q.1Amino acid no=78. What is the axil length of the peptide bond?

We know 3.6 amino acid is present per turn and the pitch is 5.4A

 For 78 amino acid  number of turns are 78/3.6=21.6

The axial length is =No. of turns in 78 amino acid x pitch 
=21.6x5.4 =117 A

Q2. In proteins, hydrogen bonds forms as follows: Donor (D)-H— Acceptor (A). Hydrogen bond is more favourable if the angle between D-H and A is:

a. <90º
b. 180º
c. >180º
d. 120º

Ans: b – 180º

Hydrogen bond: A very weak bond formed by the electrostatic attraction between hydrogen which is covalently bonded to an elPectro negative atom, such as oxygen or nitrogen, to other electro negative atom. Hydrogen bond is most favourable and strong when all the three bonded atoms are in a straight line (180º). 

Note- Proline is an imino acid which is called as helix breaker. 

Polar residues  are situated at the surface of the molecule where they can associate with the surrounding water. 

Non-polar residues are situated in the core of the molecule. 

3.Unfolding of regular secondary structure causes -------------in the entropy of the protein.

a.Increase

b.Decrease

c.May increase or decrease 

d.None of the aboveu

Ans. A

4.

Which of the following amino acids are more likely to occur in alpha helices?

(A) A,E,L,M

(B) P,G,Y,S

(C) A,G,Y,W

(D) A,C,G,S

Ans.A

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